After Wilson flipped the switch, the only QB in the NFL that was close to his level of efficiency was RG3. Wilson is also forty times less expensive for the next 3 seasons than Rodgers. He's several years younger, he's more of a running threat, better intangibles, etc. Trading Wilson for Rodgers would be like trading Mike Trout for Miguel Cabrera. Both are really damn good, but that misses the point. The Angels would be morons to trade Trout for Cabrera.
Pretty much the only argument against having Wilson #1 is just the uncertainty factor. Rodgers is a fully proven commodity, both in terms of performance and health. Wilson isn't quite there yet, so that adds a degree of risk. I think his performance is the real deal, and he's stayed very healthy in his five college plus NFL seasons, but at 5'10+", you never know. Short, mobile QBs are notorious for being injury prone (Jeff Garcia, Michael Vick, Steve Young, etc). Wilson knows how to protect his body and has a certain talent for turning what should be crushing blows into glancing hits, so I think his injury risk isn't that bad. But again, we can't know for sure after just 1 NFL season.
Regardless, Wilson should be #1. I'd probably have RG3 #2. I think most defenses would rather face Rodgers than a healthy RG3, and RG3 is far less expensive than Rodgers over the next four NFL seasons. RG3 was basically having the best season ever by a mobile QB before his injury. He's also just 23 years old.